Run away, My little Spy
by Jess's Stories
Summary: Clary had left her father, Valentine. Valentine was the most, well-known person that lived to go against the Clave, the ruling body of the shadowhunters, a league of spies dedicated to hunting the injustice in the shadows. Clary left to keep her loved ones safe from his power. She knew he wanted her, and he was going to have to fight, if he wants to win. Rated T to be safe. AU
1. Chapter 1: Welcome

Clary had gotten the order to go and spread the news of the new initiates coming in later that day. She went around all of the New York institute and handed out the flyer that said she was taking over the new group, and would be her responsibility. Clary was always amazed at how well the institute always looked. So elegant, and shiny, strange for a spy agency. She walked around just admiring the dangly chandeliers and the marble floors, to the old Victorian elevator. For a spy agency, it was quite a conflicting image.

Clary had joined the agency mostly of out desperation. She had to run away. She ran away from her father. Valentine. He was so cruel. He never cared about her wellbeing, he only wanted money and power. Clary's mother, Jocelyn, had left Valentine when she was young and left Clary to defend herself, but Clary has kept close contact to Jocelyn. Jocelyn had said, '_You can't come Clary. You have no idea how much I want to bring you with. But it's not the right time. If Valentine finds you're gone, he'll kill you. Wait until I say.' _Clary waited until she couldn't anymore. Valentine had left New York one weekend, and Clary made her escape. Valentine thinks she's dead, only because of the agency. She has to stay undercover. Clary left out of desperation, because Valentine had gone too far. Valentine had started to kill people to get his company on top, and to keep _others_ quiet. Clary had left and sent a letter to her mother. She told Jocelyn that she had to leave because she was afraid she was next, if she made a wrong move. Jocelyn understood and accepted it. Jocelyn thought it was fine, not great, but doable. Clary thought maybe by joining the agency she would be able to defend herself and hurt Valentine if needed, and it would be a great cover for her, from him.

Clary had gone to her room to dress "properly", according to her head agent, Hodge Starkweather. She went up to her room, and changed into her gear, consisting of lots of leather, especially black leather. She decided since no body was coming for a while that she could sit and draw. Clary loved to draw. She would draw whenever she could, any time of the day, every day. She never got to draw many places of the institute. Like the greenhouse, or the wide-open kitchen, or even the small but cozy living room. She had the first door on the left room, upstairs. She figured the recruits could have the rooms around her, since there's so many of them, why not put them around her so she can bug them. But as much time as she has spent there, she never really took in the beauty of it all.

After Clary had finished her drawing of her room, she decided that she would head off to the training room. She had just walked in when her phone went off. "Hello?" she asked. "Clary, you're new recruits are here," Hodge said to her with a stern voice. Clary thought Hodge was always a little on edge all the time. "I'm coming." With that she clicked off her phone and headed down stairs. She walked down stairs to see two boys and one girl. There was a black haired man about 18 years old, with a sporty build and a strong senses, from what she could tell he would be good with a bow, not really needed but nice to be able to uses a bow. Next, there was a girl about Clary's age, long black hair and was wearing heels. Clary thought the girl would be very feisty and has a great arm, good for bats and whips. Last, there was this boy about 17 years old and had golden blonde hair. Golden eyes and looked as if he had a trick up his sleeve, but seems distant. He looks as if he close with them all, so Clary suspects they're all family. '_I hope they can work well under pressure,_' Clary thought.

"Hello, and welcome to the New York Institute. This is the HQ of the Shadowhunter's Spy Agency. We do have other locations listed in the office if you would like transfer. We call ourselves shadowhunters mostly because we hunt in the shadows. We look for justice unidentified, and make sure it is taken. This is Clary, our top instructor. She will be training you for your missions to come." Hodge introduced them to this whole operation and Clary found that they we're slightly ecstatic but at the same time confused. "Hi, I'm Clary," Clary politely said. The blonde boy spoke up first, "Hi I'm Jace, and that's Alec and that's his sister, Isabelle." Both Alec and Isabelle said hello and kept quiet. "Well, can I give you the tour?" Clary asked being as nice as possible. "That would be lovely," Jace replied. Clary thought that Jace was almost flirting with her.

"As Hodge said I am your instructor, so this is where you'll be sleeping. These are your rooms, you all can pick which room you get." Isabelle went straight for the one across from me. Jace went to the one next to me on the right and Alec to the one next to Jace. They all settled and never came out again. So, Clary went to find Hodge.

Clary left the corridor and headed back down stairs. She thought that if they really wanted a tour they would find her and let her know. But, until then she decided on that she would let Hodge know what she did and headed down to the training room.

Clary walked down to the training room and opened the heavy doors to find Jace hitting a dummy. "Well, it's good to see you found this room," Clary said with a sarcastic tone. Jace stopped what he was doing and looked straight at her almost looked as if he was hurt, but then smirked. "Well, if I'm going to be better than you I need to get as much as training as I can get," Jace remarked. Clary grabbed a knife and through it. It landed right in the bull's eye on the dummy and had scraped Jace's ear. "You-"Jace stopped himself and continued, "nice hit." Clasy smiled, "thanks." She grabbed her weapons and continued what she wanted to do as Jace finished his practice and headed out. "She's not bad...," Jace said under his breath.


	2. Chapter 2: New Identities

**_A/n: Thank you, to who added this to their favorite and follow list and to who reviews, I appreciate it a lot. So, thank you very much :) Hope you will continue to read and review please, because I would like to know what you think of where it should go and your opinions. So enjoy! :D_**

Clary had gotten up pretty early to wake the recruits. "Rise and shine, recruits!" She heard what sounded like two people fall out of bed and one get up and out nicely. She guessed whoever gotten up nicely would be the one to come out first. Of course, it was Jace. "Morning!" he said as he went around Clary and headed downstairs. "Breakfast is ready…," Clary began as Jace left and Alec and Isabelle came out of their rooms. All of them were wearing their gear and ready to go.

When Clary had reached the bottom of the steps and entered the kitchen all of them were already eating and chatting. It wasn't until Clary turned behind her to see Hodge was there and they recruits got quiet. "Morning Hodge!" Clary spoke up. "Good morning," he said quietly. Hodge sat down and began to eat when he noticed the recruits were staring at him. "Well, you may continue eating, I'm not stopping you." And with that they all continued to eat, in silence.

After breakfast Clary cleaned the plates and gathered her team to lead them to the training room. "This is where you'll be training, with me. Now, you are allowed to come here any time you like but most training is done every day from 7 am till about noon, then you'll be in the class room with Hodge learning about the rules and regulations and what our job is. Alright, everybody pair up." Alec immediately grabbed Jace and Jace shrugged his shoulders at Isabelle. "Well, Isabelle it looks like you're going to be with me," Isabell looked around and didn't seem to mind. "That's fine and just call me Izzy." Clary nodded and grabbed throwing knives to begin.

"We're going to start with something easy, throwing knives. When you grab the hilt, grab it, but don't give it a death grip. When you throw, don't fling your wrist and let the dagger fly out of your hand. This shall give you pretty good aim and precision." Jace, Alec and Izzy all threw knives with excellence and it didn't take long for them to learn. "Good job," was all Clary could say.

They continues with the basics of balance, throwing, striking, hitting, blocking, stealth, anything that would give them a good foundation for Jonathan, her brother, would take over. "Well, well, what do we have here, new recruits?" he said with a smirk, wide on his face. "Everyone, this is my brother Jonathan, he'll eventually train you as well. I'm only for basics and specialized training later on."

Jonathan just looked at them all and nodded, "they will be good when we start missions again." Hodge came in and ordered Jonathan to leave. "Goodbye," he said, and left. Clary still couldn't believe he was her brother. He was stocky and muscle like their father but frail and fragile like their mother, Jocelyn. He had snow white hair had a love for stealth and merciless killing, by a few accidents on missions.

When Clary first arrived she found her brother already her. He was abounded years ago, because Valentine wouldn't let Jonathan do his bidding. But, when Clary arrived he seemed to have forgiven their father and moved on, but Clary always thought he was just waiting to strike.

Clary couldn't help but watch her brother walk away so obedient, it didn't seem like him. _'Maybe he is starting to break,'_ she thought. She ridded the thought and continued her teachings, but she couldn't help but notice that Jace was staring at her the whole time.

When they had finished she heard her phone ring. "Hello?" All she heard was silence and finally he spoke, "Clary? Hey! Um, Rebecca is back in town and I was wondering if you and your family would like to come over and have a huge welcome home party?" And Clary couldn't help but smile and her best friend, Simon. His sister has been going to college away from New York was coming home, so he wanted to know if she would come over to help him set up the decorations, in her own words. "Yes, Simon I will come over and bring Luke and mom." _'Luke,'_ she thought, '_I should go see if he's at the shop.' _"Alright see ya later Fray!" and he clicked off.

Jace being nosey piped up. "Who was that?" She turned around to face him as Izzy and Alec were cleaning up and putting away the weapons. "A friend of mine, Simon, his sister is coming back today from being out of state and wants to throw her a party," she said as she gave a smile. Jace smiled back, "well I guess we'll see you there," and turned away and left. "Wait…Jace what?!"

Clary realized that they were probably going to come so she decided she had to figure out how to apologize to Simon for the unexpected inconvenience. But, first to see Luke. She went down a couple block from her apartment to find a little run down shop full of books and supplies, including a couple weapons here and there. "Luke?" She walked around the store to find him sleeping in the back on a couch. She looked over to see her bag was still here from the last time she spent the night here. "Huh-what? Clary? Oh, what are you doing here?" She grabbed her bag and shoved him in the stomach with her knee, to wake him up. "Well, for starter waking you up, second getting my bag, and third Simon is having a party for his sister and he wants us there, all of us." He looked at her and sighed. Clary always thought he looked a little shaggy but strong and caring. He had beady eyes but a softness in the heart. "Fine, I'll go." She jumped and hugged him, "thank you." He hugged her back and she went started to head home.

She was walking home when she noticed some people heading into a club; she noticed that they looked familiar. She followed them in and tried to blend in with the crowd. She kept her distance and watched them. They approached a man and questioned him, until they stabbed him. Clary almost screamed, but what stopped her, she couldn't believe. The people that were there were her recruits, all three of them. Jace, Alec and Izzy.


	3. Chapter 3: He's Back

Clary didn't know what to think. Her recruits just questioned a man, dragged him to a closet and killed him. _'No one noticed,'_ she thought. Clary ran out of the club and headed to Simon's house. _'They killed a man, cold blooded too. But, they knew how to kill without a sound made, they have training. Why, are they here then?'_ Clary thought. She had one thought after another go around her head, dizzying her by the second. She had a point, she decided she must found out.

Clary arrived at Simon's house, to find that his sister Rebecca answered the door. "Hey, Clary! It's good to see you!" Rebecca hugged Clary and welcomed her in the house. Clary hugged Rebecca back and walked into the living room to find Simon and his mom laughing. "Hey, Fray. What's up?" Simon asked. "Well, I need to talk to you about what you called me about." Simon's mom, Elaine, smiled, but Rebecca had a questioning look on her face, but dismissed the thought. Simon, was about six feet tall, brown hair and eyes, and wore big framed glasses. Rebecca was about as tall as Simon and had the same brown eyes, which seemed to shimmer in the sun. Clary doesn't really remember how she mean Simon. She just figured he was there one day and has stayed since. Of course, Simon and Luke know of her being a spy, and so does her mom, Jocelyn, they all understood and was fine with her reasoning.

"So, what's up?" Clary panicked. She didn't want to tell Simons, but she had to, and there's the whole dead body thing. Clary knew she couldn't tell anyone about the body, so she swore she wouldn't. "So, I got Luke and mom to come, but I may have a few friends come as well," she said with a smile. "Clary!" Clary smiled a little less with Simon's retort. "What, they invited themselves! And, they may not be as bad as you think." Simon gave her a stern look. He didn't really want them there, but he reasoned. "Fine. Just let me know, who's coming, before you show up, please and thank you." Clary smiled and nodded like a six year old does when they're given a favor to do.

Clary came down stair and left, so Simon could catch up, for his sister's absence. Clary headed back toward the Institute when she heard her name being called, by a man over at the street corner. "Who's there?" The man walks toward. Clary realizes who it is. Jonathan. "Clary…what are you doing out here so late?" Clary thought about criticizing him, but he is one not to judge without him judging you more. "Well, I had to go talk to Simon about the party he's throwing for his sister." Jonathan nodded his head and backed off of Clary a little, but not enough to make it feel less awkward for her. "Very well. You shouldn't be out here so late, but for that reason I will let this slide. Hodge wants you back now, by the way." Clary watched as her brother disappeared into the fog rolling in. "Okay."

Clary had entered the Institute to find all three of her "friends" talking to Hodge. "Clary! Where have you been?" Clary came in and took off her bag. "Um, I went to see Simon. He's arranging a party for his sister, now how many times do I have to say that?!" Hodge shook his head, "I don't need you running around, when Valentine is out there, ready to kill you any second." Clary snapped. _'Hodge was never there for me, so why is he now?' _she thought. "Really Hodge? You care about me? That's nice to know." Hodge shook his head again, and everyone else stepped back away from the boiling pot called Clary. "Clary, I'm sorry, that none of us were there to protect you. It would've been best if your mother took you with her, but she didn't, and I am truly sorry, but he's made an appearance again." Clary stopped lashing out and looked at her recruits, then back at Hodge, questioning whether he was telling the truth, and if they should hear this. "Hodge, what do you mean?" Hodge gave her a sorrow filled smile, "he made a kill, with his signature." Clary had started to break down, as Jace and his siblings had just stood there speechless.

Clary had gone from a sob to a full on cry. Valentine was a rogue spy. He did want he wanted and didn't care about your opinion on it. His "operations" considered of trying to "fix" the Clave, according to him. Valentine once had tried to take down the Clave but didn't succeed, but he did create the Circle. The Circle was a group of spies, including Hodge, Jocelyn and Luke, that were trying to change the Clave but that's not easily done. Since the fall, he has been trying to do it all on his own, and since Clary didn't go with her mother, she was left to do the dirty work.

'_No, no this can't be happening. I thought…I thought he stopped. I should've known.'_ Clary thought. Hodge was trying to comfort her when Jace stepped up. "Clary. Clary! You'll be fine. I've been spy for over a third of my life and I will do anything to protect you. You understand?" Clary stopped crying. She blinked a couple of times and it hit her. _'He's been doing this for over a third, he has had training, liars. How can he protect me, when I can't even trust him?'_ she thought again as Jace had started to pull her up. "Okay, Jace." Jace picked her up and brought her over to a chair. Jace could see the horror and confusion in her face, he never felt so bad for a girl he barely knew, but maybe it wasn't sympathy, but empathy. Jace's face changed. He went for someone caring about this girl, to someone full of rage. "Jace where are you going?" Alec said as he caught Jace trying to leave the Institute. "To find Valentine."


	4. Chapter 4: The New Circle

_**A/n: SO, since I just realized this, and not many people will read my profile. I do not own The Mortal Instruments. Disclaimer done. Enjoy!**_

"Do you really think you can defeat him?" Alec had said has he caught up to Jace. "It's worth a shot." Alec knew where this was going. "Jace, don't. Don't do this. I don't want this to be like last time. Maybe we should tell her." Jace spun around to face Alec was furious, "Alec! It won't be like last time, I promise. I would rather not tell Clary but, you might be right." Alec nodded his head as Jace walked out into the night to find Valentine.

"Clary?" Clary heard whispers of her name. She opened her eyes to see Simon, Izzy and Alec staring at her. "Clary?" She finally realized that Simon was calling her. "Simon?" Everyone sighed in relief, she was alive. Clary sat up, "what happened?" Simon looked at Izzy and Alec. He got up and let Alec sit down. "Simon, knows more than he should, for not being a spy but this concerns a lot about you, by the way you were out for two days. Stress. Is a deadly poison. Anyway, Jace left to find Valentine. And, were not exactly what we say we are." Clary blinks her eyes and looks at Simon, he seems tense, like he wouldn't know Clary's reaction. "I know." They all look at her in surprise. "You do?" Izzy asked. "Yeah," Clary said shyly.

"When I left Simon's house to come back here, I saw you three go into that club, and I followed you. When I went in, I saw you three talking to some guy, and then you killed him. I ran out as soon as I could, so you wouldn't recognize me and came back here." They all had their mouths open, even Simon. "You knew?" Isabelle questioned. "Why didn't you say something? This could've been better!" Clary questioned Izzy in her head. '_Izzy what are you talking about?'_ It seems Alec heard her. "Izzy, isn't exactly herself. A while ago, we were hunting-," Alec stopped and thought about what to say, "let me start from the beginning." Clary nodded and got up out of the bed.

They walked to the library. As Clary showed Alec the way, he began, "My family comes from a line rogue spies, we do deeds no one else would. '_Justice is in our hands,' _as the motto goes. We were called to find a girl with red hair in New York, now we know it's you. We were told she was of importance, since '_her father was Valentine._' We were told Valentine was the leader of the Circle, a group that went against the Clave to try and bring a new order. We were told to find her and bring her on our side so we could bring down Valentine. That was our job, and now I'm not sure if it was successful.

"Izzy is upset because on trying to find you, Jace got in a few problems with some people that worked for Valentine and our little brother Max got in the way and was killed. Iz, doesn't want Jace to end up like Max. We killed that guy because he worked for Valentine. Clary, we're not normal spies. We're rogues." Clary stopped in front of the weapons room. "Why are we here?" Clary turned around to Alec. "Look, I don't care what you were, it depends on now what you do, if I like you or not. At some point we all go rogue, but at some point we all go back. I've already done that, now you all get too. Join me, join us. And we'll together bring down my father. He never was my father anyway." Clary walked away from Alec and went to find Hodge. Alec stood there thinking, contemplating her words, '_at some point we all go back, I've already done that.'_ "She went rogue to Valentine, but reclaimed herself here. She has come back."

Jace looked around for something that might lead to Valentine. Anything a normal spy wouldn't see. "Jonathan?" he whispered. Jonathan was there talking to some man. "We're near Simon's house. What is he doing here?" The man left and Jonathan was alone. Jace jumped from the tree he was in. "Jonathan!" Jonathan turned his head and looked at Jace. "Jace, it's nice to see you, but why are you here?" Jace smirked. "You must know who I am? 'Jace the best rogue out there!' You must've see the headlines." Jonathan smirked. "Well, then you must know I'm not one of popularity, I like the shadows." Jonathan had begun to leave when Jace stuck a knife to his throat.

"Look, I now you're working for Valentine, I know everything you said to Clary was a lie, she never really did anything. So, don't come back." Jace left, he knew Jonathan would send his message along. Jace walks in and finds Clary carrying weapons from one room to another. "What are you doing?" Clary looks at him. "Ask Alec." Clary points to where the library is. Jace follows the finger and finds Izzy, Alec and Simon all chatting with Hodge. "Jace! Welcome my boy, you're just in time," Hodge says as Jace feels a hand on his head. "Hello Jace." Izzy turns around and runs up to a woman. "MOM!" Hodge sets his stuff down and follow her. "Hello, Maryse." Maryse looks around. "Hello, it's good to be back."

Alec and Izzy catch up with Maryse while Hodge talks to Clary about her plan. "So, do you know her plan?" Jace asked. Simon looks up, "well, I guess you don't really know her yet if you can't figure it out." Jace looks down shadily upon Simon, "I know her plan; I just don't like it. I was hoping she had a different I didn't know about." Simon nods his head, "me too."

Everyone gathers together and Clary begins, "Well, yes Valentine is my father, but no I don't consider him my own. Jonathan is my brother, but again, never as my own. What I'm saying is, I never really trusted either of them. I never really did anything for Valentine and found it hard to believe that Valentine would throw away his son, "who had no potential". All I'm saying is, I want to know everything you got on him and my brother. I have feeling they are working together, and I'm willing to bring them down, but I need some help. So, will you join the Shadowhunter, and reclaim your name?" Izzy and Alec were the first to speak, then Hodge then Maryse. "Yes." Clary looked over to see her mother and Luke standing there, hand in hand, and saying yes. "Jace?" Clary heard Izzy ask. He was the only who hadn't said anything. "Jace!" Alec said. 'I don't know…"


	5. Chapter 5: He knows

_**A/n: Hey! I'm so sorry it took me a while to write this chapter. School started so I don't have as much time, but I will finish this story. I love it too much to stop. :P so, enjoy and please review and I hope you love it just as much as me. :) **_

"What do you mean, 'you don't know?'" Clary asked. Jace looked around and knew he had at least 10 pairs of eyes on him. Jace knew he had to pick his words carefully. _'If I say that I up for it, then that means I'm okay with her plan, when I'm not. But, if I say I'm not with it, they'll think I'm a traitor or at least Clary, Izzy and Alec will,'_ Jace thought. "Fine. I'll follow your plan Clary, but just know I don't like it. I will claim my name as Shadowhunter, and I will join your institute Hodge, but, what exactly do you plan to do Clary, just hit Valentine and Jonathan until their knocked out?" Clary shook her head. "To be honest, I never thought I would make it this far." Everyone except Alec and Jace started laughing, the boys just sighed.

"First of all Jace, I need to know what you have about Valentine and Jonathan. Second, then I'll give you a plan." Jace nodded. "All we really have is that they still lead the group called the Circle." Jocelyn gasped, "He still has that running? But, Valentine can't be running it, he trusts no one." Jace nodded again. "You're right. Jonathan has been running the Circle, but Valentine keeps a close eye on it himself." Clary was deep in thought, when something dawned on her. "Wait, The Circle, when my father was running it was all about changing the Clave, and he didn't succeed. So, what is Jonathan trying to accomplish?" Jace shrug his shoulders. "We have no idea. He's been keeping the Circle in the shadows and working there, we haven't seen much of him doing any activity with the group, yet. But, we all feel that he has been "building" up reputation, recruits, the list goes on. Literally, he's trying to get his name out there, and to reclaim its status." Luke shook his head. "I don't like this. Valentine let his son take over? Valentine must not be able to run it himself, either mentally or physically." Jocelyn nodded in agreement.

They all agreed on that Valentine cannot run the Circle, and Jonathan has taken over for him. "So, Clary, what did your father exactly do?" Simon asked. "We can handled that question," Maryse spoke up. Everyone looked at Maryse who had her eyes on Jocelyn, Luke and Hodge. They all nodded to let her know she can speak of, the past. "When the Circle was in formation, he recruited us. Luke, Hodge, Jocelyn, the Herondales, me and your father, Izzy and Alec. All we did, was recruit and train shadowhunters to fit Valentine's guidelines. He thought that the Clave should be removed and a new order placed, although he may be right, he did not choose that right way to execute his plan. When we had gotten enough to maybe take down the Clave, we were defeated and he ran, left us all, except Jocelyn and Luke, they ran with him. But, we forgive each other. He has been in hiding for years since, until he found Jocelyn again."

"I only left him, because I didn't want Clary his world, in this one. But, Valentine found us and took her. I told her that I left him because I didn't love him when really he took her from me. He came to me and told me if I didn't give her up he would kill me and Jonathan. I wasn't worried about me, nor Jonathan. But, of course, he knew me, he knew how to get in my head. He threaten Luke, and all of us. He would kill us slowly, and we 'would never know'. That I wouldn't stand so I let him take her, and Clary I'm sorry, I really am." Clary looked horrified at her mother. _'How could she just give me up? Am I worth nothing? Anything?'_ Clary thought. "Mom…no, I can't get mad, nor can say I'm upset on what you did. I'm just surprised and confused, but you were willing to give mine, and I lived, to save others. In a way, I don't mind but in a way I can't stand that. All I know is that my mother gave me up so I could live, and so could of you. He brought me to this world, but treated me as if I was a slave, not a daughter, he treated Jonathan like a soldier. He never made me do anything, just be there. He made Jonathan do everything, until he left.

"He told me he left because he couldn't take Valentine, but I wonder if he was kicked out. Once, he left I was left ding everything. Like, getting supplies, training, and making trades. I couldn't take all the pressure anymore so I left. Valentine never looked for me, because he went back to Jonathan, and now he's giving the orders." Alec nodded, "well, this explain a lot." Everyone stood there silent. No one knew what to say, everything was already said.

"Well, I guess the plain now, is to prepare ourselves. Gather supplies and keep training. We are not even where we need to be to defeat Valentine or Jonathan." They all agreed. Everyone disbanded and continued talking, especially the elders, of course catching up. Jace thought something was off with Clary, he went to ask. "Clary!" She turned. "Can I talk to you, somewhere private?" Clary nodded her head, took Jace's hand and lead him to the greenhouse.

"Clary…I don't believe you." Clary squinted her face. "What do you mean?" Jace looked at her with annoyance. "I mean, I don't believe your story. Your mother's seems believable but yours? Living with Valentine and you didn't do anything except be a housewife? Yeah, right. You did things with Jonathan. You did jobs for Valentine. Again, I don't believe you." Clary smirked. "You're good, Jace, almost too good. We'll see how far you'll get, and if anyone will believe you."

She walked away leaving a rhythm of steps on the concrete. Jace couldn't believe it, the girl he started to feel sorry for, was always playing a game. "She's trained to be a spy, and she's doing it good. You better run away, my little spy, or I will hurt you. I can't believe I almost fell for you."

_**OOOOH! Where will I take this? Clary is now a bad girl ;) she's the spy. Oooh! Plot twist! Well I hope you guys liked it. What will happen if everyone find out? And, does Jace feel something? Who knows! See ya later ;) -Jess p.s. do you like this twist? I would really like to know!**_


	6. Chapter 6: Let's Talk

Jace watched Clary walk out of the greenhouse. He knew she was trouble, but he couldn't help it. There was something about her. The way she moved or how she held herself high; she wasn't afraid. But, Jace knew he couldn't deny what he felt. It was like a spark lit up inside him. He had to leave when he was young.

'_I can still remember that day, the day I left him. I left Valentine. I did jobs with Jonathan and Valentine, and I never saw Clary. I didn't even know she was there, but her story doesn't fit. She can't sit still when she sets her mind. But, she admitted it, she was doing something. 'I'm good, but not that good,' damn. Clary is…she's something. I remember, she would go out at night. Sneak around. Jonathan disappeared, and Clary starts sneaking out. Humph, they're all working together. But, Jocelyn and Luke, don't know…? Well, they can find out.'_ Jace just paced around the room. He didn't know what to think. He liked Clary, a lot, but he couldn't trust her. He's in too deep, in all of this. Between her and her father and his past.

'_I was brought up by Valentine. I worked with him, and when I couldn't take it anymore and he threw me out I found Maryse. She took me in, and I've been in good business. Then I found out we were rogues, and then I found out about the Institute. It changed me, all of us. And, I'm thankful, but Clary. She's like a drug now, completely. How I know she's bad, but oh how much I do want her,' _Jace thought.

He walked down and found everyone packing and gathering as much material as the Institute had, and could hold. He saw Clary, she smirked at him. He walked over to Alec. "What's wrong?" he asked. "Clary." Alec looked at him, questionly. "What about her?" Jace shook his head, "she's not…exactly what you think." Alec squinted his eyes. "I mean, she's not…she's a special spy. Not just for us." Alec looked shocked. "You mean…?" Jace nodded. Clary looked over, as almost she heard them, loud and clear. They went back to work. Clary dismissed her feeling.

'_Damn. Jace is too good, for himself. He may know something. And, I can't hold on, that much longer. Stupid Jonathan, getting himself into messes, he shouldn't. I never asked for this, telling lies, trying to protect my family. Mom, Luke and him. He's not worth my time. But, he's like a fire, burning a hole in me. Jonathan, hurry up.'_

Clary knew that no one understood. And, that everyone thought she was a traitor. But, she was trying to protect someone, right? That's just? _'Jace, I'm sorry, please forgive me.'_

Maryse and Jocelyn had started making dinner, as everyone else gathered and started to chat and reconnect. Clary had walked toward the door, when someone grabbed her wrist and forcefully turned her around. "Where are you going?" Clary couldn't believe who she saw. It was certain blue eyed man. "Alec! What?!" Alec could hear her nervousness in her voice. She wasn't a good liar. "Where. Are. You. Going?" Alec looked at Clary as if she was pest. "Fine, since I can't win. Out. To fix what I started." Alec shook his head with his arms crossed. "Do what you want, but. Stay away from Jace." Clary smirked and started walking out the door. She was on the sidewalk away from the door, and Alec was closing it when, "Oh, Alec? Do send Jace a kiss for me." And she was gone. Alec was beyond sock, he couldn't believe what she heard, and he knew what she meant. Two things: one, she's realized he's gay; two, he realized she like Jace. Alec walked backed in, to find a happy concerned Jace. "Hey, what's wrong?" Alec puts on a smile. "Nothing. I thought I heard something."

Clary ran down the street to meet Valentine. She walked into an abandon factory. "VALENTINE!" she screamed. Valentine laughed, and walked down a staircase off in the distance. Clary didn't like the drab, mud and dust all over the place. Garbage and rats here and there. And, nothing but rusted metal, with some new plumbing. Plus, everything's black, as coal. "Well, my little fiery rogue is back. Jonathan? Come out." Jonathan came out with chains wrapped around his body. He could barely move, and with a good piece of tape over his mouth, he couldn't speak. "I got them to start your plan. Let some chains off, or let me talk to him. Please." Valentine shook his head, and walked over to a couch. He waved his hand and Jonathan was taken away. "See, I can't do that. They're not here, and I don't trust you or your brother, daughter. Nice story, by the way. Saying, you were housewife. You wish you were."

Clary understood quite well. Her "lie" wasn't as white, as some may think. She did live with Valentine, but she wasn't a housewife. She was a sort of everything. She would hull the loads, deal with the money, recruit spies. She did everything, even a housewife. But, she never did anything like Jonathan or Jace did. "Yes, you remember quite well."

Clary heard a bang at the door. More, and more. Someone was trying to come in. "Grab my son, and hide him. Well? Go!" Two bodyguards grabbed Jonathan and took off. Jonathan sprang and had out a knife. He grabbed Clary and put it to her throat, when the door swung open.

It had to be at least almost eight o'clock before Jace could tell Clary was gone. "Alec? Izzy! Izzy, where's Clary?" Izzy was almost drunk, "slightly off", as some put it. "I d-don't…kno-know," she said with hiccups. "I saw-her..leave..earlier..be-fore we…ate." Jace was sober enough to understand enough. She left. He wasn't going to let her go. _'She's too innocent, she never…I don't know.'_ He found Alec and made him tell Jace where she went. "I don't know!" Jace dismissed him in disgust. "Jace! She never cared about you. If she did, it was all a lie." Jace waved him away. He ran, and ran until he found a bodyguard that seemed familiar from when he worked with Valentine and followed him. He barged in.

"Jace! Welcome, son," Valentine said as he released Clary. Clary ran under his arm and into the corner. She couldn't believe he was here. She wiped her neck, and saw red on her hands. She had a slight slit from Valentine. "Clary," Jace whispered. She shook her head, and walked over to grab the bodyguards and Jonathan. "Sit down, let's talk," Valentine said as all four of them sat down. At least Jonathan wasn't tied up.


	7. Chapter 7: The Little Spy

"Look, my son, my daughter, my _other_ son. We're all here. How wonderful!"

Jonathan hissed in disgust. "'My _other s_on', I appreciate the love, f_ather._"

Valentine smirked. "Now, let's set the record straight, shall we?" Clary sighed. She knew exactly what this meant.

"So, let's see. Jonathan and _Jonathan_ both worked for me since they were young, but you, Jace, by accident. I remember you were a little boy with no family, and I took you in. Now, Clary you left around the time Jace came in. See, Jace, your family was getting in the way of my "dealing", so I took them out. You were helpless, and me being merciful, I took you in and raised you, and you learned well.

"But you, _Jonathan_, were too rough, impressive, but obvious. Now, _Clarissa_, how do you fit? Well, you did almost everything for me, since _your mother _left. I was hurt, but she didn't care, we were so close to bringing down the Clave. So close, but no she didn't care. So, you filled her spot. While they went did the outside job, you got stuck inside. _My little spy._ Thanks, for the letters, they helped." She touched her throat, she noticed it was getting worse.

"Clary, what letters?" Jace asked.

"I've been…sending letter…regarding our plan, to bring him down."

Jonathan got up from the seat, and sat next to Valentine. "They were very helpful, little sister."

"No…you LIAR!" Clary got up and almost hit him, when the same bodyguards holding Jonathan held her.

"What is she talking about?" Jace asked.

"I spent months trying to get information on how the Clave planned to take down _my father._ She did it so well, I figure I play along, until I'm not needed and wait. Say, I got captured. She never knew. I worked for him."

"How could you?! I spent hours trying to save you by getting that information, and you were undercover. You…monster!"

Clary stopped fighting the man and sunk into his arms. Jace was in shock, his face froze and he would not say anything,

'_She was trying to do the right thing…we both survived…we both left. She's…a whole burning in me,' _Jace thought.

"But, please Clarissa, won't you join me?" Valentine asked.

"_**Never,"**_she hissed.

Valentine waved his hands and both she and Jace were sent down to the cellar.

"Jace, I'm sorry." He looked up from his shaking hands. She sat across from him, in the same cell.

"For what?"

She was almost in tears. "For everything. I pulled you into this. I lied to you, and pretended to be someone I'm not. I just…"

Jace took he hand. "Clary, in the time I've known you, you're different. You put up a fight, you do what you think is right. So, what, as long as you're willing to fix and end what you started, I'll be there. But, you need to set _everyone _straight." She nodded.

Clary noticed the door was ajar, and that there was crowbar not far from them. She started pushing her arm through the bars to try and grab the crowbar. "What are you doing?"

"You'll see," Clary said with sly smile. Jace smirked.

'_I have to get him out of this. He can't be back in this…come on, just a little closer!'_ Clary thought. Clary grabbed he crowbar, and pulled in through. She jammed it into the bars, and pushed and pushed to break the rusted ones. She was able to get almost half broken almost to the top, enough to slip through.

"Okay, there's a back entrance, we go out there," she whispered. Jace nodded.

Clary couldn't help but look, stare, into his eyes. The way they would shine even if there was no light. How, golden and bright they were, making that hole bigger.

She knew she had to finish this. But, she wasn't ready to do it with him. Clary took Jace to the back entrance. "Go! I'll be right there!" Jace went out and Clary shut and locked the door. "Clary!"

Clary did it for herself, for him. "Jace, I'm sorry, I have to finish this…I don't want you to get hurt…" and she ran off.

'_Stupid Clary…I don't want you to get hurt. I'm sorry, I was so cold.'_ He ran off to get Alec and Izzy.

"Valentine!" Clary screamed.

Jace ran down the road again and took the long way back. He needed to think. '_Stupid Clary, can't she see? Alec was wrong, it was never a lie. Her acting was,' _He thought.

When he finally arrived, most people were asleep or past out, from the party. He found Alec, sober. "Alec!" Alec looked at him with anger.

"Clary! She's going after Valentine. Now!" Alec shook his head. "So? She hurt you, me.

She didn't care about any of us, can't you see that?" Jace's eyes began to water.

"No, can't you? She thought she was doing the right thing, she thought Jonathan was captured. Remember how she changed because Jonathan left? It was because Jonathan did…for Valentine. Clary got some information to save him, in reality Jonathan was always trying to get it. Clary can be trusted, not him."

Alec didn't know what to think. He had to trust Jace, since they were _parabatai._ "Fine. But, she has to explain this, to all of us. I can't trust her, but I can you. Get Izzy, we do this alone."

"In the end, it didn't matter huh? He would've gotten it anyway. I just made things easier."

Valentine smirked. He wasn't surprised that she was able to escape, but that she didn't bring Jace.

"So, you left your boyfriend?" Jonathan said.

"He's not…" Clary looked down, at her hands. How he held hers, how she felt, how he did. It all clicked.

"Really? 'Cause he seems to think so…" Clary nodded. They can't know, _never. _

"Well, then join me sister, we call rule this world. Make things anew. Please. For father," he said with a concerning tone.

She shook her head and pushed him away. "I left so I could get away, and not to join again, "when I'm ready to accept it"."

Jonathan spat on her face. "Fine, I asked. You said no," he grabbed a knife.

Valentine put his hand on his son's shoulder, "Jonathan, no. She must live."

Jonathan understood, and left Clary alone, confused and irritated.

"Izzy come on!" She struggled against him. "Why? Leave me alone!"

Jace picked her up and dragged her to Alec. "Deal with your sister." She snapped. "I'm yours too!" Jace smiled.

"Come on, Iz."

They got their gear, and headed toward the factory. "There," Jace pointed out.

They stealthy walked down to the factory and woke Izzy up. "Izzy, wake up," Alec said.

"Huh? Where are we?" She said as she grabbed her head, because of her pounding headache.

"We're going to rescue Clary," Alec said, trying to wake his sister.

"Look, over there!" Jace pointed out to Clary being pushed to a ledge.

"Well, since you won't help us, you wouldn't mind if I get rid of you?" Valentine said, as he grabbed Clary's arm and dragged her out to the ledge and started to push her farther and farther with a gun.

"I've delt with you, for too long. Good bye, Clarissa."

"No, please. Valentine please!"

"Father, please. We can use her." Jonathan grabbed his father's hand.

"NO! I've wasted so much on her! Her and Jocelyn. I shouldn't be mad at you and yet, _I AM_."

Valentine knocked back his son, and punched him out cold. He continued to push Clary to the edge. "You, should've left with your mother."

"No, I shouldn't have." Clary kicked the gun out of his hand. "No, I'm glad I stayed. It made me realize you don't know a thing, about _me." _She had the gun pointed at him. "I learned quite well, who you are, and who you'll always be. I learned that my mother was right, and that my dad was Luke, you were _never _there. Now, this isn't some daughter-father thing, no, this is about your ideas and how I'm in the way. You won't ever see me again. Valentine. _Ever." _

Clary fired once and ran. The bullet hit Valentine right in the shoulder. "_Run away, my little spy. Run away."_

Jace heard the gun. He thought the worst until he her scream and be dragged out by the guards. "Come on!" They all ran, even Izzy. The gun firing had woken her up, good.

"Clary!" Clary turned her head to see Jace running and Alec helping Izzy not far behind him.

"Jace…" Clary's throat had stopped bleeding, but her other wounds from trying to fight the guards that picked her up and was taking her somewhere, somewhere she didn't know.

Jace had kicked the man holding her, and he let her go. She scrambled to her feet and grabbed the knife Jace was holding. She threw the knife and it landed in his back. The other guard had come around the corner and tried to shoot Jace and Clary when the gun went off and they both saw the bullet hit the building.

"Alec…" Clary said. Alec had fired his bow and the arrow landed right in the man's chest.

"Come on, I don't want to be here, when the cops come." Clary followed Jace. Alec and Izzy followed them as they made their way back to the Institute.

**_A/n: Hey! I'm sorry for the long wait! I thought I wrote this, but when I went to go write "chapter 8", I noticed I never did this, so I wrote it. Well, I hope you guys liked it! I hope, I set the record straight. soon, we will have Clace fluff! SO, I hope you're as excited as me! SO, my apologies, I give you this long chapter! :D -Jess_**


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